BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080674.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 834,971 number of mapped reads = 763,037 (91.38%) number of supplementary alignments = 6,220 (0.74%) number of secondary alignments = 0 number of mapped bases = 52,324,344 bp number of sequenced bases = 52,304,305 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,101 duplication rate = 2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9189 >>>>>>> ACTG content number of A's = 14,857,788 bp (28.41%) number of C's = 9,537,193 bp (18.23%) number of T's = 16,730,625 bp (31.99%) number of G's = 11,176,364 bp (21.37%) number of N's = 2,335 bp (0%) GC percentage = 39.6% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 369,563 number of insertions = 4,198 mapped reads with insertion percentage = 0.55% number of deletions = 12,295 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.99% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 0.1545X There is a 1.55% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6319411 0.02535364194739559 0.18656678157096776 chr2 243199373 3535932 0.014539231562903742 0.16641989555159983 chr3 198022430 3394278 0.01714087641485866 0.1390780451653242 chr4 191154276 2187727 0.011444823761096509 0.1150160544676109 chr5 180915260 2412995 0.013337708494020903 0.12267943784155606 chr6 171115067 3193160 0.018660893257284 0.16224794926571906 chr7 159138663 3190521 0.0200486854662088 0.24483884190919028 chr8 146364022 6347777 0.04336979069897382 0.2465600630058994 chr9 141213431 1661910 0.011768781398704208 0.1258003189767411 chr10 135534747 2518602 0.018582703371261687 0.1486411095557061 chr11 135006516 2281531 0.01689941395124958 0.14304981254241464 chr12 133851895 1723634 0.012877172938044695 0.12100021606583722 chr13 115169878 1123444 0.009754668664318634 0.10532725235196512 chr14 107349540 1008985 0.009399062166451762 0.10395768881600052 chr15 102531392 918177 0.008955081776320758 0.10217112129115612 chr16 90354753 1253708 0.013875396239531528 0.1269058651503308 chr17 81195210 765828 0.009431935701625748 0.1049722428472111 chr18 78077248 1696121 0.021723626836847528 0.17911658189051816 chr19 59128983 727906 0.012310477249371937 0.12483446219856682 chr20 63025520 1283720 0.02036825717582338 0.153080921923384 chr21 48129895 751446 0.015612874285306461 0.1340713506991203 chr22 51304566 482752 0.009409532866918707 0.1031741529601944 chrMT 16571 5886 0.35519884134934526 0.6829606986513533 chrX 155270560 3445723 0.02219173422186408 0.16164073612776703 chrY 59373566 93170 0.0015692168464329732 0.043995571158438704